public virtual void TestNumberOfUnplacedHeavyAtoms_IAtomContainer()
{
var ac = MakeAlphaPinene();
var count = new AtomPlacer3D().NumberOfUnplacedHeavyAtoms(ac);
Assert.AreEqual(10, count);
}
public virtual void TestNumberOfUnplacedHeavyAtoms_IAtomContainerWithExplicitHydrogens()
{
var ac = MakeMethaneWithExplicitHydrogens();
var count = new AtomPlacer3D().NumberOfUnplacedHeavyAtoms(ac);
Assert.AreEqual(1, count);
}
public void TestGetBondLengthValue_String_String()
{
var parser = CDK.SmilesParser;
var smiles = "CCCCCC";
var molecule = parser.ParseSmiles(smiles);
Assert.IsNotNull(molecule);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mmff94");
AtomPlacer3D atomPlacer3d = new AtomPlacer3D(ffc.GetParameterSet());
ffc.AssignAtomTyps(molecule);
string id1 = molecule.Atoms[1].AtomTypeName;
string id2 = molecule.Atoms[2].AtomTypeName;
string mmff94id1 = "C";
string mmff94id2 = "C";
Assert.AreNotSame(mmff94id1, id1);
Assert.AreNotSame(mmff94id2, id2);
double bondlength = atomPlacer3d.GetBondLengthValue(id1, id2);
Assert.AreEqual(1.508, bondlength, 0.001);
}
public void TestGetNextPlacedHeavyAtomWithUnplacedRingNeighbour_IAtomContainer()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer acyclicAlkane = TestMoleculeFactory.MakeAlkane(3);
IAtomContainer cycloPentane = TestMoleculeFactory.MakeCyclopentane();
//TestMoleculeFactory does not set ISINRING flags for cyclic molecules
Assert.AreEqual(false, cycloPentane.Atoms[0].IsInRing);
foreach (var atom in cycloPentane.Atoms)
{
atom.IsInRing = true;
}
//acyclic molecule so null is expected
foreach (var atom in acyclicAlkane.Atoms)
{
atom.IsPlaced = true;
}
Assert.IsNull(atmplacer.GetNextPlacedHeavyAtomWithUnplacedRingNeighbour(acyclicAlkane));
for (int j = 0; j < 3; j++)
{
cycloPentane.Atoms[j].IsPlaced = true;
}
Assert.AreEqual(cycloPentane.Atoms[2],
atmplacer.GetNextPlacedHeavyAtomWithUnplacedRingNeighbour(cycloPentane));
}
public void TestGetUnplacedRingHeavyAtom_IAtomContainer_IAtom()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeCyclopentane();
foreach (var atom in molecule.Atoms)
{
atom.IsInRing = true;
}
for (int j = 0; j < 2; j++)
{
molecule.Atoms[j].IsPlaced = true;
}
IAtom atom0 = molecule.Atoms[0];
IAtom atom1 = molecule.Atoms[1];
IAtom natom = molecule.Atoms[4];
IAtom atom0pair = atmplacer.GetUnplacedRingHeavyAtom(molecule, atom0);
IAtom atom1pair = atmplacer.GetUnplacedRingHeavyAtom(molecule, atom1);
IAtom natompair = atmplacer.GetUnplacedRingHeavyAtom(molecule, natom);
Assert.AreEqual(atom0pair, molecule.Atoms[4]);
Assert.AreEqual(atom1pair, molecule.Atoms[2]);
Assert.AreEqual(atom0.IsPlaced, true);
foreach (var bond in molecule.Bonds)
{
if (bond.GetOther(molecule.Atoms[4]) != null &&
!bond.GetOther(molecule.Atoms[4]).IsPlaced)
{
natompair = bond.GetOther(molecule.Atoms[4]);
}
}
Assert.AreEqual(natompair, molecule.Atoms[3]);
}
public void TestFindHeavyAtomsInChain_IAtomContainer_IAtomContainer()
{
var filename = "NCDK.Data.MDL.allmol232.mol";
var ins = ResourceLoader.GetAsStream(filename);
// TODO: shk3-cleanuptests: best to use the STRICT IO mode here
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile);
var ac = new Silent.AtomContainer(containersList.First());
AddExplicitHydrogens(ac);
var chain = ac.Builder.NewAtomContainer();
for (int i = 16; i < 25; i++)
{
chain.Atoms.Add(ac.Atoms[i]);
}
chain.Atoms.Add(ac.Atoms[29]);
chain.Atoms.Add(ac.Atoms[30]);
int[] result = new AtomPlacer3D().FindHeavyAtomsInChain(ac, chain);
Assert.AreEqual(16, result[0]);
Assert.AreEqual(11, result[1]);
}
public virtual void TestGetPlacedHeavyAtom_IAtomContainer_IAtom()
{
var ac = MakeAlphaPinene();
var acplaced = new AtomPlacer3D().GetPlacedHeavyAtom(ac, ac.Atoms[0]);
Assert.IsNull(acplaced);
ac.Atoms[1].IsPlaced = true;
acplaced = new AtomPlacer3D().GetPlacedHeavyAtom(ac, ac.Atoms[0]);
Assert.AreEqual(ac.Atoms[1], acplaced);
}
public void TestAllHeavyAtomsPlaced_benzene()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer benzene = TestMoleculeFactory.MakeBenzene();
foreach (var atom in benzene.Atoms)
{
atom.IsPlaced = true;
}
Assert.IsTrue(atmplacer.AllHeavyAtomsPlaced(benzene));
}
public override void TestNumberOfUnplacedHeavyAtoms_IAtomContainer()
{
IAtomContainer molecule = TestMoleculeFactory.MakeAlkane(5);
for (int i = 0; i < 3; i++)
{
(molecule.Atoms[i]).IsPlaced = true;
}
int placedAtoms = new AtomPlacer3D().NumberOfUnplacedHeavyAtoms(molecule);
Assert.AreEqual(2, placedAtoms);
}
public void TestIsHeavyAtom()
{
var ac = MakeMethaneWithExplicitHydrogens();
var carbon = ac.Atoms[0];
var hydrogen = ac.Atoms[1];
var placer = new AtomPlacer3D();
bool result = false;
result = placer.IsHeavyAtom(carbon);
Assert.IsTrue(result);
result = placer.IsHeavyAtom(hydrogen);
Assert.IsFalse(result);
}
public void InvalidChain()
{
string input = "CCCCCC(CCCC)CCCC";
var sp = CDK.SmilesParser;
var m = sp.ParseSmiles(input);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mmff92");
ffc.AssignAtomTyps(m);
AtomPlacer3D ap3d = new AtomPlacer3D(ffc.GetParameterSet());
ap3d.PlaceAliphaticHeavyChain(m, m);
}
public void TestGetNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour_IAtomContainer()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer cyclobutane = TestMoleculeFactory.MakeCyclobutane();
IAtomContainer acyclicAlkane = TestMoleculeFactory.MakeAlkane(6);
foreach (var atom in cyclobutane.Atoms)
{
atom.IsInRing = true;
}
foreach (var atom in acyclicAlkane.Atoms)
{
atom.IsAliphatic = true;
}
for (int j = 0; j < 3; j++)
{
cyclobutane.Atoms[j].IsPlaced = true;
}
IAtom nextHeavyAtom = atmplacer.GetNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(cyclobutane);
Assert.IsNull(nextHeavyAtom);
foreach (var atom in cyclobutane.Atoms)
{
if (!atom.IsPlaced)
{
atom.IsPlaced = true;
}
}
IAtom nextHeavyAtom2 = atmplacer.GetNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(cyclobutane);
Assert.IsNull(nextHeavyAtom2);
for (int k = 0; k < 3; k++)
{
acyclicAlkane.Atoms[k].IsPlaced = true;
}
IAtom nextSuchUnplacedHeavyAtom = atmplacer.GetNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(acyclicAlkane);
Assert.AreEqual(acyclicAlkane.Atoms[3], nextSuchUnplacedHeavyAtom);
foreach (var atom in acyclicAlkane.Atoms)
{
atom.IsPlaced = true;
}
nextSuchUnplacedHeavyAtom = atmplacer.GetNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(acyclicAlkane);
Assert.IsNull(nextSuchUnplacedHeavyAtom);
}
public void TestGetFarthestAtom_Point3d_IAtomContainer()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeBenzene();
molecule.Atoms[0].Point3D = new Vector3(0.0, 0.0, 0.0);
molecule.Atoms[1].Point3D = new Vector3(1.0, 1.0, 1.0);
molecule.Atoms[4].Point3D = new Vector3(3.0, 2.0, 1.0);
molecule.Atoms[5].Point3D = new Vector3(4.0, 4.0, 4.0);
IAtom farthestFromAtoma = atmplacer.GetFarthestAtom(molecule.Atoms[0].Point3D.Value, molecule);
IAtom farthestFromAtomb = atmplacer.GetFarthestAtom(molecule.Atoms[4].Point3D.Value, molecule);
Assert.AreEqual(molecule.Atoms[5], farthestFromAtoma);
Assert.AreEqual(molecule.Atoms[0], farthestFromAtomb);
}
public override void TestGetPlacedHeavyAtoms_IAtomContainer_IAtom()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeBenzene();
for (int j = 0; j < 3; j++)
{
(molecule.Atoms[j]).IsPlaced = true;
}
IAtomContainer placedAndConnectedTo1 = atmplacer.GetPlacedHeavyAtoms(molecule, molecule.Atoms[1]);
IAtomContainer placedAndConnectedTo2 = atmplacer.GetPlacedHeavyAtoms(molecule, molecule.Atoms[2]);
IAtomContainer placedAndConnectedTo4 = atmplacer.GetPlacedHeavyAtoms(molecule, molecule.Atoms[4]);
Assert.AreEqual(2, placedAndConnectedTo1.Atoms.Count);
Assert.AreEqual(1, placedAndConnectedTo2.Atoms.Count);
Assert.AreEqual(0, placedAndConnectedTo4.Atoms.Count);
}
public override void TestGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeAlkane(7);
for (int j = 0; j < 5; j++)
{
molecule.Atoms[j].IsPlaced = true;
}
IAtom atom2 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[1], molecule.Atoms[0]);
IAtom atom3 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[2], molecule.Atoms[1]);
IAtom nullAtom = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[0], molecule.Atoms[1]);
Assert.AreEqual(atom2, molecule.Atoms[2]);
Assert.AreEqual(atom3, molecule.Atoms[3]);
Assert.IsNull(nullAtom);
}
public override void TestGeometricCenterAllPlacedAtoms_IAtomContainer()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeAlkane(2);
foreach (var atom in molecule.Atoms)
{
atom.IsPlaced = true;
}
molecule.Atoms[0].Point3D = new Vector3(-1.0, 0.0, 0.0);
molecule.Atoms[1].Point3D = new Vector3(1.0, 0.0, 0.0);
Vector3 center = atmplacer.GeometricCenterAllPlacedAtoms(molecule);
Assert.AreEqual(0.0, center.X, 0.01);
Assert.AreEqual(0.0, center.Y, 0.01);
Assert.AreEqual(0.0, center.Z, 0.01);
}
public void TestGetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour_IAtomContainer()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer benzene = TestMoleculeFactory.MakeBenzene();
IAtomContainer acyclicAlkane = TestMoleculeFactory.MakeAlkane(5);
foreach (var atom in benzene.Atoms)
{
atom.IsInRing = true;
}
foreach (var atom in acyclicAlkane.Atoms)
{
atom.IsAliphatic = true;
}
for (int j = 0; j < 3; j++)
{
benzene.Atoms[j].IsPlaced = true;
}
IAtom searchedatom1 = atmplacer.GetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(benzene);
Assert.IsNull(searchedatom1);
foreach (var atom in benzene.Atoms)
{
if (!atom.IsPlaced)
{
atom.IsPlaced = true;
}
}
IAtom searchedatom2 = atmplacer.GetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(benzene);
Assert.IsNull(searchedatom2);
for (int k = 0; k < 3; k++)
{
acyclicAlkane.Atoms[k].IsPlaced = true;
}
IAtom nextAtom = atmplacer.GetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(acyclicAlkane);
Assert.AreEqual(acyclicAlkane.Atoms[2], nextAtom);
}
public override void TestGetPlacedHeavyAtom_IAtomContainer_IAtom()
{
AtomPlacer3D atmplacer = new AtomPlacer3D();
IAtomContainer molecule = TestMoleculeFactory.MakeCyclohexane();
// For(IAtom a : m.Atoms) a.IsPlaced = true;
for (int i = 0; i < 3; i++)
{
molecule.Atoms[i].IsPlaced = true;
}
IAtom atom1 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[0]);
Assert.AreEqual(atom1, molecule.Atoms[1]);
IAtom atom2 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[2]);
Assert.AreEqual(atom2, molecule.Atoms[1]);
IAtom atom3 = atmplacer.GetPlacedHeavyAtom(molecule, molecule.Atoms[4]);
Assert.IsNull(atom3);
}
public void TestGetAngleValue_String_String_String()
{
var parser = CDK.SmilesParser;
var smiles = "CCCCCC";
var molecule = parser.ParseSmiles(smiles);
Assert.IsNotNull(molecule);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mmff94");
AtomPlacer3D atomPlacer3d = new AtomPlacer3D(ffc.GetParameterSet());
ffc.AssignAtomTyps(molecule);
string id1 = molecule.Atoms[1].AtomTypeName;
string id2 = molecule.Atoms[2].AtomTypeName;
string id3 = molecule.Atoms[3].AtomTypeName;
double anglev = atomPlacer3d.GetAngleValue(id1, id2, id3);
Assert.AreEqual(109.608, anglev, 0.001);
}
public virtual void TestGeometricCenterAllPlacedAtoms_IAtomContainer()
{
var ac = MakeAlphaPinene();
for (int i = 0; i < ac.Atoms.Count; i++)
{
ac.Atoms[i].IsPlaced = true;
}
ac.Atoms[0].Point3D = new Vector3(1.39, 2.04, 0);
ac.Atoms[0].Point3D = new Vector3(2.02, 2.28, -1.12);
ac.Atoms[0].Point3D = new Vector3(3.44, 2.80, -1.09);
ac.Atoms[0].Point3D = new Vector3(3.91, 2.97, 0.35);
ac.Atoms[0].Point3D = new Vector3(3.56, 1.71, 1.16);
ac.Atoms[0].Point3D = new Vector3(2.14, 2.31, 1.29);
ac.Atoms[0].Point3D = new Vector3(0, 1.53, 0);
ac.Atoms[0].Point3D = new Vector3(2.83, 3.69, 1.17);
ac.Atoms[0].Point3D = new Vector3(3.32, 4.27, 2.49);
ac.Atoms[0].Point3D = new Vector3(2.02, 4.68, 0.35);
var center = new AtomPlacer3D().GeometricCenterAllPlacedAtoms(ac);
Assert.AreEqual(2.02, center.X, 0.01);
Assert.AreEqual(4.68, center.Y, 0.01);
Assert.AreEqual(0.35, center.Z, 0.01);
}
/// <summary>
/// Generate 3D coordinates with force field information.
/// </summary>
public IAtomContainer Generate3DCoordinates(IAtomContainer molecule, bool clone)
{
var originalAtomTypeNames = molecule.Atoms.Select(n => n.AtomTypeName).ToArray();
Debug.WriteLine("******** GENERATE COORDINATES ********");
foreach (var atom in molecule.Atoms)
{
atom.IsPlaced = false;
atom.IsVisited = false;
}
//CHECK FOR CONNECTIVITY!
Debug.WriteLine($"#atoms>{molecule.Atoms.Count}");
if (!ConnectivityChecker.IsConnected(molecule))
{
throw new CDKException("Molecule is NOT connected, could not layout.");
}
// setup helper classes
AtomPlacer atomPlacer = new AtomPlacer();
AtomPlacer3D ap3d = new AtomPlacer3D(parameterSet);
AtomTetrahedralLigandPlacer3D atlp3d = new AtomTetrahedralLigandPlacer3D(parameterSet);
if (clone)
{
molecule = (IAtomContainer)molecule.Clone();
}
atomPlacer.Molecule = molecule;
if (ap3d.NumberOfUnplacedHeavyAtoms(molecule) == 1)
{
Debug.WriteLine("Only one Heavy Atom");
ap3d.GetUnplacedHeavyAtom(molecule).Point3D = new Vector3(0.0, 0.0, 0.0);
try
{
atlp3d.Add3DCoordinatesForSinglyBondedLigands(molecule);
}
catch (CDKException ex3)
{
Trace.TraceError($"PlaceSubstitutensERROR: Cannot place substitutents due to:{ex3.Message}");
Debug.WriteLine(ex3);
throw new CDKException("PlaceSubstitutensERROR: Cannot place substitutents due to:" + ex3.Message,
ex3);
}
return(molecule);
}
//Assing Atoms to Rings,Aliphatic and Atomtype
IRingSet ringSetMolecule = ffc.AssignAtomTyps(molecule);
IRingSet largestRingSet = null;
int numberOfRingAtoms = 0;
IReadOnlyList <IRingSet> ringSystems = null;
if (ringSetMolecule.Count > 0)
{
if (templateHandler == null)
{
throw new CDKException("You are trying to generate coordinates for a molecule with rings, but you have no template handler set. Please do SetTemplateHandler() before generation!");
}
ringSystems = RingPartitioner.PartitionRings(ringSetMolecule);
largestRingSet = RingSetManipulator.GetLargestRingSet(ringSystems);
IAtomContainer largestRingSetContainer = RingSetManipulator.GetAllInOneContainer(largestRingSet);
numberOfRingAtoms = largestRingSetContainer.Atoms.Count;
templateHandler.MapTemplates(largestRingSetContainer, numberOfRingAtoms);
if (!CheckAllRingAtomsHasCoordinates(largestRingSetContainer))
{
throw new CDKException("RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be layout.");
}
SetAtomsToPlace(largestRingSetContainer);
SearchAndPlaceBranches(molecule, largestRingSetContainer, ap3d, atlp3d, atomPlacer);
largestRingSet = null;
}
else
{
//Debug.WriteLine("****** Start of handling aliphatic molecule ******");
IAtomContainer ac = AtomPlacer.GetInitialLongestChain(molecule);
SetAtomsToUnVisited(molecule);
SetAtomsToUnplaced(molecule);
ap3d.PlaceAliphaticHeavyChain(molecule, ac);
//ZMatrixApproach
ap3d.ZMatrixChainToCartesian(molecule, false);
SearchAndPlaceBranches(molecule, ac, ap3d, atlp3d, atomPlacer);
}
LayoutMolecule(ringSystems, molecule, ap3d, atlp3d, atomPlacer);
//Debug.WriteLine("******* PLACE SUBSTITUENTS ******");
try
{
atlp3d.Add3DCoordinatesForSinglyBondedLigands(molecule);
}
catch (CDKException ex3)
{
Trace.TraceError($"PlaceSubstitutensERROR: Cannot place substitutents due to:{ex3.Message}");
Debug.WriteLine(ex3);
throw new CDKException("PlaceSubstitutensERROR: Cannot place substitutents due to:" + ex3.Message, ex3);
}
// restore the original atom type names
for (int i = 0; i < originalAtomTypeNames.Length; i++)
{
molecule.Atoms[i].AtomTypeName = originalAtomTypeNames[i];
}
return(molecule);
}
/// <summary>
/// Layout all aliphatic chains with ZMatrix.
/// </summary>
/// <param name="startAtoms">AtomContainer of possible start atoms for a chain</param>
private void PlaceLinearChains3D(IAtomContainer molecule, IAtomContainer startAtoms, AtomPlacer3D ap3d,
AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer)
{
//Debug.WriteLine("****** PLACE LINEAR CHAINS ******");
IAtom dihPlacedAtom = null;
IAtom thirdPlacedAtom = null;
IAtomContainer longestUnplacedChain = molecule.Builder.NewAtomContainer();
if (startAtoms.Atoms.Count == 0)
{
//no branch points ->linear chain
//Debug.WriteLine("------ LINEAR CHAIN - FINISH ------");
}
else
{
for (int i = 0; i < startAtoms.Atoms.Count; i++)
{
//Debug.WriteLine("FOUND BRANCHED ALKAN");
//Debug.WriteLine("Atom NOT NULL:" + molecule.Atoms.IndexOf(startAtoms.GetAtomAt(i)));
thirdPlacedAtom = ap3d.GetPlacedHeavyAtom(molecule, startAtoms.Atoms[i]);
dihPlacedAtom = ap3d.GetPlacedHeavyAtom(molecule, thirdPlacedAtom, startAtoms.Atoms[i]);
longestUnplacedChain.Atoms.Add(dihPlacedAtom);
longestUnplacedChain.Atoms.Add(thirdPlacedAtom);
longestUnplacedChain.Atoms.Add(startAtoms.Atoms[i]);
longestUnplacedChain.Add(AtomPlacer.GetLongestUnplacedChain(molecule, startAtoms.Atoms[i]));
SetAtomsToUnVisited(molecule);
if (longestUnplacedChain.Atoms.Count < 4)
{
//di,third,sec
//Debug.WriteLine("------ Single BRANCH METHYLTYP ------");
//break;
}
else
{
//Debug.WriteLine("LongestUnchainLength:"+longestUnplacedChain.Atoms.Count);
ap3d.PlaceAliphaticHeavyChain(molecule, longestUnplacedChain);
ap3d.ZMatrixChainToCartesian(molecule, true);
SearchAndPlaceBranches(molecule, longestUnplacedChain, ap3d, atlp3d, atomPlacer);
}
longestUnplacedChain.RemoveAllElements();
}//for
}
//Debug.WriteLine("****** HANDLE ALIPHATICS END ******");
}
/// <summary>
/// Search and place branches of a chain or ring.
/// </summary>
/// <param name="chain">AtomContainer if atoms in an aliphatic chain or ring system</param>
private void SearchAndPlaceBranches(IAtomContainer molecule, IAtomContainer chain, AtomPlacer3D ap3d,
AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer)
{
//Debug.WriteLine("****** SEARCH AND PLACE ****** Chain length: "+chain.Atoms.Count);
IAtomContainer branchAtoms = molecule.Builder.NewAtomContainer();
IAtomContainer connectedAtoms = molecule.Builder.NewAtomContainer();
for (int i = 0; i < chain.Atoms.Count; i++)
{
var atoms = molecule.GetConnectedAtoms(chain.Atoms[i]);
foreach (var atom in atoms)
{
if (!atom.AtomicNumber.Equals(AtomicNumbers.H) & !atom.IsPlaced & !atom.IsInRing)
{
connectedAtoms.Add(ap3d.GetPlacedHeavyAtoms(molecule, chain.Atoms[i]));
try
{
SetBranchAtom(molecule, atom, chain.Atoms[i], connectedAtoms, ap3d, atlp3d);
}
catch (CDKException ex2)
{
Trace.TraceError($"SearchAndPlaceBranchERROR: Cannot find enough neighbour atoms due to {ex2.ToString()}");
throw new CDKException($"SearchAndPlaceBranchERROR: Cannot find enough neighbour atoms: {ex2.Message}", ex2);
}
branchAtoms.Atoms.Add(atom);
connectedAtoms.RemoveAllElements();
}
}
}//for ac.getAtomCount
PlaceLinearChains3D(molecule, branchAtoms, ap3d, atlp3d, atomPlacer);
}
/// <summary>
/// Sets a branch atom to a ring or aliphatic chain.
/// </summary>
/// <param name="unplacedAtom">The new branchAtom</param>
/// <param name="atomA">placed atom to which the unplaced atom is connected</param>
/// <param name="atomNeighbours">placed atomNeighbours of atomA</param>
private static void SetBranchAtom(IAtomContainer molecule, IAtom unplacedAtom, IAtom atomA, IAtomContainer atomNeighbours,
AtomPlacer3D ap3d, AtomTetrahedralLigandPlacer3D atlp3d)
{
//Debug.WriteLine("****** SET Branch Atom ****** >"+molecule.Atoms.IndexOf(unplacedAtom));
IAtomContainer noCoords = molecule.Builder.NewAtomContainer();
noCoords.Atoms.Add(unplacedAtom);
Vector3 centerPlacedMolecule = ap3d.GeometricCenterAllPlacedAtoms(molecule);
IAtom atomB = atomNeighbours.Atoms[0];
string atypeNameA = atomA.AtomTypeName;
string atypeNameB = atomB.AtomTypeName;
string atypeNameUnplaced = unplacedAtom.AtomTypeName;
double length = ap3d.GetBondLengthValue(atypeNameA, atypeNameUnplaced);
double angle = (ap3d.GetAngleValue(atypeNameB, atypeNameA, atypeNameUnplaced)) * Math.PI / 180;
// Console.Out.WriteLine("A:"+atomA.Symbol+" "+atomA.AtomTypeName+
// " B:"+atomB.Symbol+" "+atomB.AtomTypeName
// +" unplaced Atom:"
// +unplacedAtom.AtomTypeName+" BL:"+length+" Angle:"+angle
// +" FormalNeighbour:"
// +atomA.FormalNeighbourCount+" HYB:"+atomA.getFlag
// (CDKConstants.HYBRIDIZATION_SP2)
// +" #Neigbhours:"+atomNeighbours.Atoms.Count);
IAtom atomC = ap3d.GetPlacedHeavyAtom(molecule, atomB, atomA);
Vector3[] branchPoints = atlp3d.Get3DCoordinatesForLigands(atomA, noCoords, atomNeighbours, atomC,
(atomA.FormalNeighbourCount.Value - atomNeighbours.Atoms.Count), length, angle);
double distance = 0;
int farthestPoint = 0;
for (int i = 0; i < branchPoints.Length; i++)
{
if (Math.Abs(Vector3.Distance(branchPoints[i], centerPlacedMolecule)) > Math.Abs(distance))
{
distance = Vector3.Distance(branchPoints[i], centerPlacedMolecule);
farthestPoint = i;
}
}
int stereo = -1;
IBond unplacedBond = molecule.GetBond(atomA, unplacedAtom);
if (atomA.StereoParity != 0 ||
(unplacedBond.Stereo == BondStereo.Up || unplacedBond.Stereo == BondStereo.Down) &&
molecule.GetMaximumBondOrder(atomA) == BondOrder.Single)
{
if (atomNeighbours.Atoms.Count > 1)
{
stereo = AtomTetrahedralLigandPlacer3D.MakeStereocenter(atomA.Point3D.Value, molecule.GetBond(atomA, unplacedAtom),
(atomNeighbours.Atoms[0]).Point3D.Value, (atomNeighbours.Atoms[1]).Point3D.Value,
branchPoints);
}
}
if (stereo != -1)
{
farthestPoint = stereo;
}
unplacedAtom.Point3D = branchPoints[farthestPoint];
unplacedAtom.IsPlaced = true;
}
/// <summary>
/// Layout the ring system, rotate and translate the template.
/// </summary>
/// <param name="originalCoord">coordinates of the placedRingAtom from the template</param>
/// <param name="placedRingAtom">placedRingAtom</param>
/// <param name="ringSet">ring system which placedRingAtom is part of</param>
/// <param name="centerPlacedMolecule">the geometric center of the already placed molecule</param>
/// <param name="atomB">placed neighbour atom of placedRingAtom</param>
private static void LayoutRingSystem(Vector3 originalCoord, IAtom placedRingAtom, IRingSet ringSet,
Vector3 centerPlacedMolecule, IAtom atomB, AtomPlacer3D ap3d)
{
//Debug.WriteLine("****** Layout ring System ******");Console.Out.WriteLine(">around atom:"+molecule.Atoms.IndexOf(placedRingAtom));
IAtomContainer ac = RingSetManipulator.GetAllInOneContainer(ringSet);
Vector3 newCoord = placedRingAtom.Point3D.Value;
Vector3 axis = new Vector3(atomB.Point3D.Value.X - newCoord.X, atomB.Point3D.Value.Y - newCoord.Y, atomB.Point3D.Value.Z - newCoord.Z);
TranslateStructure(originalCoord, newCoord, ac);
//Rotate Ringsystem to farthest possible point
Vector3 startAtomVector = new Vector3(newCoord.X - atomB.Point3D.Value.X, newCoord.Y - atomB.Point3D.Value.Y, newCoord.Z - atomB.Point3D.Value.Z);
IAtom farthestAtom = ap3d.GetFarthestAtom(placedRingAtom.Point3D.Value, ac);
Vector3 farthestAtomVector = new Vector3(farthestAtom.Point3D.Value.X - newCoord.X, farthestAtom.Point3D.Value.Y - newCoord.Y, farthestAtom.Point3D.Value.Z - newCoord.Z);
Vector3 n1 = Vector3.Cross(axis, farthestAtomVector);
n1 = Vector3.Normalize(n1);
double lengthFarthestAtomVector = farthestAtomVector.Length();
Vector3 farthestVector = startAtomVector;
farthestVector = Vector3.Normalize(farthestVector);
farthestVector *= startAtomVector.Length() + lengthFarthestAtomVector;
double dotProduct = Vector3.Dot(farthestAtomVector, farthestVector);
double angle = Math.Acos(dotProduct / (farthestAtomVector.Length() * farthestVector.Length()));
Vector3 ringCenter = new Vector3();
for (int i = 0; i < ac.Atoms.Count; i++)
{
if (!(ac.Atoms[i].IsPlaced))
{
ringCenter.X = (ac.Atoms[i].Point3D).Value.X - newCoord.X;
ringCenter.Y = (ac.Atoms[i].Point3D).Value.Y - newCoord.Y;
ringCenter.Z = (ac.Atoms[i].Point3D).Value.Z - newCoord.Z;
ringCenter = AtomTetrahedralLigandPlacer3D.Rotate(ringCenter, n1, angle);
ac.Atoms[i].Point3D =
new Vector3(ringCenter.X + newCoord.X, ringCenter.Y + newCoord.Y, ringCenter.Z + newCoord.Z);
//ac.GetAtomAt(i).IsPlaced = true;
}
}
//Rotate Ring so that geometric center is max from placed center
//Debug.WriteLine("Rotate RINGSYSTEM");
Vector3 pointRingCenter = GeometryUtil.Get3DCenter(ac);
double distance = 0;
double rotAngleMax = 0;
angle = 1 / 180 * Math.PI;
ringCenter = new Vector3(pointRingCenter.X, pointRingCenter.Y, pointRingCenter.Z);
ringCenter.X = ringCenter.X - newCoord.X;
ringCenter.Y = ringCenter.Y - newCoord.Y;
ringCenter.Z = ringCenter.Z - newCoord.Z;
for (int i = 1; i < 360; i++)
{
ringCenter = AtomTetrahedralLigandPlacer3D.Rotate(ringCenter, axis, angle);
if (Vector3.Distance(centerPlacedMolecule, new Vector3(ringCenter.X, ringCenter.Y, ringCenter.Z)) > distance)
{
rotAngleMax = i;
distance = Vector3.Distance(centerPlacedMolecule, new Vector3(ringCenter.X, ringCenter.Y, ringCenter.Z));
}
}
//rotate ring around axis with best angle
rotAngleMax = (rotAngleMax / 180) * Math.PI;
for (int i = 0; i < ac.Atoms.Count; i++)
{
if (!(ac.Atoms[i].IsPlaced))
{
ringCenter.X = (ac.Atoms[i].Point3D).Value.X;
ringCenter.Y = (ac.Atoms[i].Point3D).Value.Y;
ringCenter.Z = (ac.Atoms[i].Point3D).Value.Z;
ringCenter = AtomTetrahedralLigandPlacer3D.Rotate(ringCenter, axis, rotAngleMax);
ac.Atoms[i].Point3D = new Vector3(ringCenter.X, ringCenter.Y, ringCenter.Z);
ac.Atoms[i].IsPlaced = true;
}
}
}
/// <summary>
/// Layout the molecule, starts with ring systems and than aliphatic chains.
/// </summary>
/// <param name="ringSetMolecule">ringSystems of the molecule</param>
private void LayoutMolecule(IReadOnlyList <IRingSet> ringSetMolecule, IAtomContainer molecule, AtomPlacer3D ap3d,
AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer)
{
//Debug.WriteLine("****** LAYOUT MOLECULE MAIN *******");
IAtomContainer ac = null;
int safetyCounter = 0;
IAtom atom = null;
//Place rest Chains/Atoms
do
{
safetyCounter++;
atom = ap3d.GetNextPlacedHeavyAtomWithUnplacedRingNeighbour(molecule);
if (atom != null)
{
//Debug.WriteLine("layout RingSystem...");
var unplacedAtom = ap3d.GetUnplacedRingHeavyAtom(molecule, atom);
var ringSetA = GetRingSetOfAtom(ringSetMolecule, unplacedAtom);
var ringSetAContainer = RingSetManipulator.GetAllInOneContainer(ringSetA);
templateHandler.MapTemplates(ringSetAContainer, ringSetAContainer.Atoms.Count);
if (CheckAllRingAtomsHasCoordinates(ringSetAContainer))
{
}
else
{
throw new IOException("RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be layout. Sorry");
}
Vector3 firstAtomOriginalCoord = unplacedAtom.Point3D.Value;
Vector3 centerPlacedMolecule = ap3d.GeometricCenterAllPlacedAtoms(molecule);
SetBranchAtom(molecule, unplacedAtom, atom, ap3d.GetPlacedHeavyAtoms(molecule, atom), ap3d, atlp3d);
LayoutRingSystem(firstAtomOriginalCoord, unplacedAtom, ringSetA, centerPlacedMolecule, atom, ap3d);
SearchAndPlaceBranches(molecule, ringSetAContainer, ap3d, atlp3d, atomPlacer);
//Debug.WriteLine("Ready layout Ring System");
ringSetA = null;
unplacedAtom = null;
}
else
{
//Debug.WriteLine("layout chains...");
SetAtomsToUnVisited(molecule);
atom = ap3d.GetNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(molecule);
if (atom != null)
{
ac = atom.Builder.NewAtomContainer();
ac.Atoms.Add(atom);
SearchAndPlaceBranches(molecule, ac, ap3d, atlp3d, atomPlacer);
ac = null;
}
}
} while (!ap3d.AllHeavyAtomsPlaced(molecule) || safetyCounter > molecule.Atoms.Count);
}
